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- EMDB-21419: E. coli ATP Synthase ADP Sub-state 3a Fo Focussed -

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Basic information

Entry
Database: EMDB / ID: EMD-21419
TitleE. coli ATP Synthase ADP Sub-state 3a Fo Focussed
Map data
Sample
  • Complex: E. coli ATP Synthase
    • Protein or peptide: ATP synthase subunit c
    • Protein or peptide: ATP synthase subunit b
    • Protein or peptide: ATP synthase subunit a
KeywordsE coli ATP Synthase / ion channel / ATPase / MEMBRANE PROTEIN
Function / homology
Function and homology information


: / proton motive force-driven plasma membrane ATP synthesis / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / hydrolase activity / lipid binding / plasma membrane
Similarity search - Function
ATP synthase, F0 complex, subunit b, bacterial / F-type ATP synthase subunit B-like, membrane domain superfamily / : / ATP synthase, F0 complex, subunit A, bacterial/chloroplast / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily ...ATP synthase, F0 complex, subunit b, bacterial / F-type ATP synthase subunit B-like, membrane domain superfamily / : / ATP synthase, F0 complex, subunit A, bacterial/chloroplast / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily / ATP synthase A chain / ATP synthase a subunit signature. / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
ATP synthase subunit a / ATP synthase subunit b / ATP synthase subunit c / ATP synthase subunit a / ATP synthase subunit b / ATP synthase subunit c
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsStewart AG / Walshe JL
Funding support Australia, 1 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Nat Commun / Year: 2020
Title: Cryo-EM structures provide insight into how E. coli FF ATP synthase accommodates symmetry mismatch.
Authors: Meghna Sobti / James L Walshe / Di Wu / Robert Ishmukhametov / Yi C Zeng / Carol V Robinson / Richard M Berry / Alastair G Stewart /
Abstract: FF ATP synthase functions as a biological rotary generator that makes a major contribution to cellular energy production. It comprises two molecular motors coupled together by a central and a ...FF ATP synthase functions as a biological rotary generator that makes a major contribution to cellular energy production. It comprises two molecular motors coupled together by a central and a peripheral stalk. Proton flow through the F motor generates rotation of the central stalk, inducing conformational changes in the F motor that catalyzes ATP production. Here we present nine cryo-EM structures of E. coli ATP synthase to 3.1-3.4 Å resolution, in four discrete rotational sub-states, which provide a comprehensive structural model for this widely studied bacterial molecular machine. We observe torsional flexing of the entire complex and a rotational sub-step of F associated with long-range conformational changes that indicates how this flexibility accommodates the mismatch between the 3- and 10-fold symmetries of the F and F motors. We also identify density likely corresponding to lipid molecules that may contribute to the rotor/stator interaction within the F motor.
History
DepositionFeb 20, 2020-
Header (metadata) releaseMar 25, 2020-
Map releaseJun 3, 2020-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 17
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 17
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6vwk
  • Surface level: 17
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21419.png

Downloads & links

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Map

FileDownload / File: emd_21419.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.08 Å/pix.
x 350 pix.
= 377.65 Å		1.08 Å/pix.
x 350 pix.
= 377.65 Å		1.08 Å/pix.
x 350 pix.
= 377.65 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.079 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 17.0 / Movie #1: 17
Minimum - Maximum-52.807217000000001 - 83.315880000000007
Average (Standard dev.)0.00000000000191 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 377.65 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0791.0791.079
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z377.650377.650377.650
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ350350350
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS350350350
D min/max/mean-52.80783.3160.000

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Supplemental data

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Sample components

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Entire : E. coli ATP Synthase

EntireName: E. coli ATP Synthase
Components
  • Complex: E. coli ATP Synthase
    • Protein or peptide: ATP synthase subunit c
    • Protein or peptide: ATP synthase subunit b
    • Protein or peptide: ATP synthase subunit a

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Supramolecule #1: E. coli ATP Synthase

SupramoleculeName: E. coli ATP Synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 558 KDa

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Macromolecule #1: ATP synthase subunit c

MacromoleculeName: ATP synthase subunit c / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 8.259064 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MENLNMDLLY MAAAVMMGLA AIGAAIGIGI LGGKFLEGAA RQPDLIPLLR TQFFIVMGLV DAIPMIAVGL GLYVMFAVA

UniProtKB: ATP synthase subunit c

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Macromolecule #2: ATP synthase subunit b

MacromoleculeName: ATP synthase subunit b / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 17.289953 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MNLNATILGQ AIAFVLFVLF CMKYVWPPLM AAIEKRQKEI ADGLASAERA HKDLDLAKAS ATDQLKKAKA EAQVIIEQAN KRRSQILDE AKAEAEQERT KIVAQAQAEI EAERKRAREE LRKQVAILAV AGAEKIIERS VDEAANSDIV DKLVAEL

UniProtKB: ATP synthase subunit b

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Macromolecule #3: ATP synthase subunit a

MacromoleculeName: ATP synthase subunit a / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 30.324096 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MASENMTPQD YIGHHLNNLQ LDLRTFSLVD PQNPPATFWT INIDSMFFSV VLGLLFLVLF RSVAKKATSG VPGKFQTAIE LVIGFVNGS VKDMYHGKSK LIAPLALTIF VWVFLMNLMD LLPIDLLPYI AEHVLGLPAL RVVPSADVNV TLSMALGVFI L ILFYSIKM ...String:
MASENMTPQD YIGHHLNNLQ LDLRTFSLVD PQNPPATFWT INIDSMFFSV VLGLLFLVLF RSVAKKATSG VPGKFQTAIE LVIGFVNGS VKDMYHGKSK LIAPLALTIF VWVFLMNLMD LLPIDLLPYI AEHVLGLPAL RVVPSADVNV TLSMALGVFI L ILFYSIKM KGIGGFTKEL TLQPFNHWAF IPVNLILEGV SLLSKPVSLG LRLFGNMYAG ELIFILIAGL LPWWSQWILN VP WAIFHIL IITLQAFIFM VLTIVYLSMA SEEH

UniProtKB: ATP synthase subunit a

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 78283
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING

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